Data last updated: 2018-08-10p12Note: Includes annotations on GRCh38.p12 patch sequences

Description

This track was created by using Arian Smit's
RepeatMasker
program, which screens DNA sequences
for interspersed repeats and low complexity DNA sequences. The program
outputs a detailed annotation of the repeats that are present in the
query sequence (represented by this track), as well as a modified version
of the query sequence in which all the annotated repeats have been masked
(generally available on the
Downloads page). RepeatMasker uses the
Repbase Update library of repeats from the
Genetic
Information Research Institute (GIRI).
Repbase Update is described in Jurka (2000) in the References section below.

Display Conventions and Configuration

In full display mode, this track displays up to ten different classes of repeats:

Short interspersed nuclear elements (SINE), which include ALUs

Long interspersed nuclear elements (LINE)

Long terminal repeat elements (LTR), which include retroposons

DNA repeat elements (DNA)

Simple repeats (micro-satellites)

Low complexity repeats

Satellite repeats

RNA repeats (including RNA, tRNA, rRNA, snRNA, scRNA, srpRNA)

Other repeats, which includes class RC (Rolling Circle)

Unknown

The level of color shading in the graphical display reflects the amount of
base mismatch, base deletion, and base insertion associated with a repeat
element. The higher the combined number of these, the lighter the shading.

A "?" at the end of the "Family" or "Class" (for example, DNA?) signifies that
the curator was unsure of the classification. At some point in the future,
either the "?" will be removed or the classification will be changed.

Methods

Data are generated using the RepeatMasker -s flag. Additional flags
may be used for certain organisms. Repeats are soft-masked. Alignments may
extend through repeats, but are not permitted to initiate in them.
See the FAQ for more information.

Credits

Thanks to Arian Smit, Robert Hubley and GIRI for providing the tools and
repeat libraries used to generate this track.